rs17882942
Variant summary
Our verdict is Likely benign. Variant got -5 ACMG points: 0P and 5B. BP4_StrongBP6
The NM_007194.4(CHEK2):c.1534C>G(p.Leu512Val) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000163 in 1,593,670 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_007194.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_benign. Variant got -5 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CHEK2 | NM_007194.4 | c.1534C>G | p.Leu512Val | missense_variant | 14/15 | ENST00000404276.6 | NP_009125.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CHEK2 | ENST00000404276.6 | c.1534C>G | p.Leu512Val | missense_variant | 14/15 | 1 | NM_007194.4 | ENSP00000385747 | P2 |
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000856 AC: 20AN: 233624Hom.: 0 AF XY: 0.0000623 AC XY: 8AN XY: 128318
GnomAD4 exome AF: 0.0000166 AC: 24AN: 1441464Hom.: 0 Cov.: 29 AF XY: 0.0000153 AC XY: 11AN XY: 717720
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152206Hom.: 0 Cov.: 32 AF XY: 0.0000134 AC XY: 1AN XY: 74358
ClinVar
Submissions by phenotype
not provided Uncertain:4
Uncertain significance, criteria provided, single submitter | clinical testing | Quest Diagnostics Nichols Institute San Juan Capistrano | Sep 18, 2023 | In the published literature, this variant has been reported in individuals affected with breast cancer (PMID: 21244692 (2011), 25186627 (2015), 31206626 (2019)), colorectal cancer ((PMID: 28944238 (2017)) as well as in unaffected individuals (PMID: 31206626 (2019)). This variant was characterized as benign based on an in vivo yeast-based functional assay (PMID: 30851065 (2019)). The frequency of this variant in the general population, 0.0006 (21/35204 chromosomes (Genome Aggregation Database, http://gnomad.broadinstitute.org)), is uninformative in the assessment of its pathogenicity. Analysis of this variant using bioinformatics tools for the prediction of the effect of amino acid changes on protein structure and function yielded predictions that this variant is benign. Based on the available information, we are unable to determine the clinical significance of this variant. - |
Uncertain significance, criteria provided, single submitter | clinical testing | GeneDx | Jun 05, 2024 | Published functional studies demonstrate no damaging effect: normal growth in response to DNA damage (PMID: 30851065); Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis indicates that this missense variant does not alter protein structure/function; Observed in individuals with a personal history of breast cancer (PMID: 21244692, 25186627); This variant is associated with the following publications: (PMID: 21244692, 26787654, 27527004, 16671833, 25186627, 31398194, 31106920, 30851065) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Women's Health and Genetics/Laboratory Corporation of America, LabCorp | May 15, 2017 | Variant summary: The CHEK2 c.1534C>G (p.Leu512Val) variant involves the alteration of a non-conserved nucleotide, resulting in a missense substitution in the protein kinase domain (InterPro). 5/5 in silico tools predict benign outcome for this variant. This variant was found in 5/113850 control chromosomes including broad and large population from ExAC at a frequency of 0.0000439, which does not exceed the estimated maximal expected allele frequency of a pathogenic CHEK2 variant (0.0003125). However, it was only found in Latino subpopulation with an allele frequency of 0.000452 (5/11054 chromosomes) which is nearly 1.5 times the estimated maximal expected allele frequency, possibly suggesting that it is a rare population-specific polymorphism. However, in a case-control study, this variant was found in one breast cancer patient but not in controls (Calvez-Kelm_2011). Pathogenic variants in this gene are associated with elevated risk of breast cancer. Whether this variant is a significant risk allele needs to be further investigated. To our knowledge, the variant has not been tested by in vitro/in vivo functional assays. Multiple clinical diagnostic laboratories/reputable databases have classified this variant as uncertain significance. Taken together, this variant is currently classified as VUS-possibly benign. - |
Uncertain significance, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Dec 12, 2016 | - - |
Familial cancer of breast Uncertain:2Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Labcorp Genetics (formerly Invitae), Labcorp | Jan 24, 2024 | This sequence change replaces leucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 512 of the CHEK2 protein (p.Leu512Val). This variant is present in population databases (rs17882942, gnomAD 0.06%), and has an allele count higher than expected for a pathogenic variant. This missense change has been observed in individual(s) with breast cancer (PMID: 21244692, 25186627). ClinVar contains an entry for this variant (Variation ID: 141856). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be tolerated. Experimental studies are conflicting or provide insufficient evidence to determine the effect of this variant on CHEK2 function (PMID: 30851065). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance. - |
Uncertain significance, criteria provided, single submitter | clinical testing | Counsyl | Mar 29, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | Myriad Genetics, Inc. | Mar 09, 2023 | This variant is considered likely benign. This variant is strongly associated with less severe personal and family histories of cancer, typical for individuals without pathogenic variants in this gene [PMID: 25085752]. - |
Hereditary cancer-predisposing syndrome Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Oct 11, 2023 | The p.L512V variant (also known as c.1534C>G), located in coding exon 13 of the CHEK2 gene, results from a C to G substitution at nucleotide position 1534. The leucine at codon 512 is replaced by valine, an amino acid with highly similar properties. This alteration has been identified in multiple individuals diagnosed with breast cancer and in controls across studies (Le Calvez-Kelm F et al. Breast Cancer Res., 2011 Jan;13:R6; Young EL et al. J. Med. Genet., 2016 06;53:366-76; Weitzel JN et al. Cancer. 2019 08;125(16):2829-2836). This variant was also reported in a cohort of 1231 colorectal cancer cases (DeRycke MS et al. Mol Genet Genomic Med. 2017 Sep;5(5):553-569). This alteration behaved as functional in an in vivo, yeast-based growth rate assay (Delimitsou A et al. Hum. Mutat., 2019 05;40:631-648). This alteration was also reported as functional in a study assessing CHEK2-complementation through quantification of KAP1 phosphorylation and CHK2 autophosphorylation in human RPE1-CHEK2-knockout cells (Stolarova L et al. Clin Cancer Res, 2023 Aug;29:3037-3050). This amino acid position is poorly conserved in available vertebrate species. In addition, this missense alteration is predicted to be tolerated by in silico analysis, but In silico splice site analysis for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Likely benign, criteria provided, single submitter | clinical testing | Color Diagnostics, LLC DBA Color Health | Jun 28, 2016 | - - |
Familial cancer of breast;C0376358:Malignant tumor of prostate;C0585442:Bone osteosarcoma;C5882668:Li-Fraumeni syndrome 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Fulgent Genetics, Fulgent Genetics | Oct 31, 2018 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at